Widow Six Seven had just given them the signal over the radio: "Cleared hot." Seconds later, a fierce roaring could be heard as the US F15 fighter jets dropped two 500lb bombs on their targets below. As one dropped a third bomb on a Taliban bunker, men could be seen on the ground desperately scrabbling out from their cover as it came under attack.

To the American pilots, the rather posh English vowels responding to their "in hot" request and guiding their missile fire over the "net" gave no clue that the army officer with whom they were communicating was in fact a member of the British royal family.

The soldier they knew only as call sign Widow Six Seven was in fact Prince Harry, working in Afghanistan as a Forward Air Controller [FAC] identifying Taliban forces on the ground, verifying coordinates and clearing them as targets for attack.

Until now, the media had agreed to a blackout on reporting that the 23-year-old Household Cavalry officer has been in Afghanistan since just before Christmas. His absence from Sandringham over the festive period was barely commented upon, nor was the lack of tabloid photographs of him leaving London nightclubs, worse for wear.

The prince had retrained as an FAC after being refused permission to fight in Iraq alongside the men he had led in his regiment as troop leader. He admits now he was regarded as a "bullet magnet". As a compromise, the soldier was allowed – under strict conditions of secrecy – to work from a fortified position a distance away from the frontline in Helmand province, calling in aircraft and observing enemy movements. In interviews prior to his deployment but not released until now, he said he had considered leaving the army after he was refused the chance to go to Iraq.

On screens known to the troops as Kill TV or Taliban TV, the prince watched live pictures of the action on the battlefield. Cornet [a special rank within the Household Cavalry] Wales, as he is known in the army, would observe all movements within his own Restricted Operating Zone [ROZ] and give jets permission to enter his airspace when he felt it was safe to do so. The prince's job was to study the pictures, looking for body heat or movement that would help pinpoint the enemy, locating Taliban bunkers, trench systems and compounds.

Sitting in the operations room at the base, he said: "Terry Taliban and his mates, as soon as they hear air they go to ground which makes life a little bit tricky. So having something that gives you a visual feedback from way up means that they can carry on with their normal pattern of life and we can follow them."

As part of his battlegroup's Fire Planning Cell, one of Harry's most important responsibilities was to prevent accidents such as planes being hit by mortars and artillery shells or becoming involved in friendly fire incidents. He carried out "pattern of life surveys" and was tasked with ensuring no civilians were on the ground when attacks took place.

"My job is to get air up, whether I have been tasked it a day before or on the day or when troops are in a contact (with the enemy). Air is tasked to me, they check in to me when they come into the ROZ and then I'm basically responsible for that aircraft," he said.

Before any strike on a target it is up to the FAC to set the co-ordinates and give final clearance to drop a bomb. Because of the constant demands for air support across southern Afghanistan, a key part of the prince's job was also to "bid" for aircraft which could be British, US, French or from another allied country. This included ensuring both regular access to surveillance jets and – if soldiers on the ground were under attack – calling in fighter planes from other parts of southern Afghanistan at short notice.

"The whole place is just deserted," said Harry, surveying the scene through the cross-sight of a 0.50mm calibre machine gun. "There are no roofs on any of the compounds, there are craters all over the place, it looks like something out of the Battle of the Somme."

The Prince's immediate boss, Major Mark Milford, Officer Commanding B Company of the 1st Battalion, the Royal Gurkha Rifles, said: "This is the southern border for the coalition troops, this is about as dangerous as it can get."

Crouching on sandbags, an open box of ammunition at the ready next to him, the prince shot at the distant puffs of smoke that marked his target.

"It's just no man's land," said Harry, peering through an arch of sandbags over the abandoned farmland, a shredded piece of sack cloth hanging in front provided the only cover for his firing position.